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Changelog

Source: NEWS.md

pmtables 0.10.1

Bugs Fixed

  • Fixed a bug in pt_data_inventory() where missing values in the by column resulted in the missing value summary row getting labeled as an “All data” summary row; this fix replaces missing values with the character string "NA" as the table is built and “All data” summary rows are now properly labeled (#373).

pmtables 0.10.0

  • Brackets in table body or table notes are now sanitized or masked by default to \lbrack or \rbrack; this behavior can be modified or turned off through an argument called mask_bracket which is passed to make_tabular() (masking brackets in the table body) or tab_notes() (masking brackets in table notes); both make_tabular() and tab_notes() can receive the mask_bracket argument through stable() or stable_long() (#367).

Bugs Fixed

  • Fixed a bug in parsing TeX glossary entries with braces around acronym options such as shortplural or longplural via read_glossary() ; parsing is now done through tools::parseLatex (#370).

pmtables 0.9.0

  • pt_demographics() was refactored (#363).

    • Include the median in the default summary function
    • Rows where Statistic is “Missing” (provided by the default summary function for continuous data) and all summary values are “0” are dropped by default
    • New argument drop_miss can be used to optionally retain the “Missing” stat for all continuous data summaries

  • pt_inventory_long() is a new function to create data inventory summaries like those generated by pt_data_inventory(), but stratified by multiple covariates (#360).

  • When a caption macro name is provided to stable_long(), it will only be used if the macro is defined; if the macro is not defined, some replacement text is included noting that the macro will be used once it is defined (#355).

pmtables 0.8.1

Bugs Fixed

pmtables 0.8.0

  • New functionality to include output file path information in the table annotation (#341).

pmtables 0.7.0

  • New functionality to create table notes from glossary files (#326).
    • read_glossary() reads from .tex or .yaml formatted files, returning a glossary object
    • select_glossary() selects specific entries from a glossary object
    • as_glossary() creates a glossary object on the fly or from a list
    • glossary_notes() creates notes from a glossary object, a list, or the name of a glossary file
    • st_notes_glo() creates and and attaches notes to a table in a pipeline
  • stable_save_image() added to create an image from a table and save to a specific location; this builds on st_aspdf() and st_aspng(), adding convenient syntax and options (#333).
  • The maxex argument to sig() can now be set through the pmtables.maxex option (#328).

Bugs Fixed

  • Fixed a bug in pt_cat_long() when the by argument is used with no all data summary (#330).

pmtables 0.6.0

  • st_caption() function added to associate a caption (including short caption and possibly a label) to any table; captions will appear in st2report() outputs; captions will always be written to file for stable_long outputs and can be optionally written to file for stable outputs (#313).

  • yaml_as_df() will now retain row names in a column named by the new argument row_var (#317).

  • st_align(), st_left(), st_right() and st_center() can now be called multiple times in a pipeline, supported by new update method for aligncol objects (#315).

  • st_clone() function added to make a copy of stobject objects (#314).

  • The id_col argument to pt_cont_long() and pt_cont_wide() is deprecated (#305).

Bugs Fixed

  • Fixed bug where sumrows was not recognized as a valid field in stobject objects (#312).

pmtables 0.5.2

  • pmtables has been updated to be compatible with stringr 1.5.0, which changed the classes of pattern modifiers (#302).

pmtables 0.5.1

Bugs Fixed

  • Fixed bug where all_name was not getting used in pt_data_inventory() (#297).

  • Fixed bug where detached table notes were getting rendered too close to the main table when building standalone pdf under certain TeX distributions (#286).

pmtables 0.5.0

pmtables 0.4.1

  • colgroup() (and st_span()) gains an align argument to position the spanner title on left or right in addition to the center (default) #260, #261.

  • rowpanel() (and st_panel()) gains jutargument to push non-panel table contents to the right relative to the panel header row so that contents under the panel header are indented #251, #253.

  • Panel header rows are now modified so that the header row stays with the first non-header row for longtable output #252, #253.

  • Consistent BQL / BLQ handling for column titles and table notes for pt_data_inventory() #254, #255.

pmtables 0.4.0

  • Add cols_omit option to omit column header data (#213)

  • Add pt_demographics function to generate a new table of both continuous and categorical data (#186, #249)

  • Add title_side argument to colsplit() so that the title can be taken from left or right side of split (#231)

  • Add hline argument to rowgroup() constructor to make the horizontal line above the panel data optional (#215)

  • Refactor pt_data_inventory() to calculate percent BLQ using denominator that is the sum of the number of observations BLQ and non-BLQ / non-missing (#221, #222)

  • st_asis() gains a method for pmtable objects (#236)

  • List names are now escaped when passing a list of tables to st2report() and friends (#232)

  • Add newline after printing table text using st_asis() (#224)

pmtables 0.3.3

  • Fix bug where arguments could not be passed along to stable_long() when coercing pmtable output (#203)

  • Fix bug where user-specified font size was not getting propagated to long table output with stable_long() (#204)

pmtables 0.3.2

  • Fix cols renaming and utilization of table argument in pt_cont_wide; add tests for column renaming for cat / cont / long / wide #199
  • Fix error message when duplicate panels are found #198

pmtables 0.3.1

  • Add .list argument to st_rename() allowing user to pass rename information as a named list with format old name = new name #189
  • Fix bug where drop_miss wasn’t executing correctly #182
  • stable_long() is now a generic function with methods for data.frame, stobject and pmtable #179
  • Expand documentation for data summary functions
  • st_span() was slightly refactored so that it would dispatch to st_span_split() when the split argument was passed #173
  • Fixed a bug where span_split() was updating column names, but this was happening before other spans were calculated #172
  • The categorical data summary functions now check for missing values (NA) and will replace them with the string "NA" and issue a warning #117

pmtables 0.3.0

  • Add landscape mode when previewing tables with st2report(), st2article() or st2doc(); see landscape argument to st_wrap() #129
  • Add lt_cap_short argument to stable_long() to set a short table title that will appear in list of tables #131
  • Fix a bug in continuous data summary tables when no observations were found in a particular group; use na_fill argument to set placeholder #133
  • Add ability to accumulate hline indices when set with st_hline() #134
  • Fix a bug in cols_bold that prevented sanitizing text prior to styling as bold #141
  • Add ability to introduce row breaks in spanner titles #143
  • Add st2report() to quickly preview tables in a real-like report document, build directly with pdflatex #148
  • Add st2article() to quickly preview tables in a latex article-like, built directly with pdflatex #148
  • Add st_asis() function and asis argument to st_wrap(); pipe tables to st_asis() or use asis argument to render tables in line in an Rmd document; in addition to formatting output “as-is”, latex dependencies are also invoked #149
  • Expand yaml_as_df() functionality to accept table columns by position, rather than name #154
  • Add stable() method for stobject #159
  • Fix bug where column spanners were not getting displayed in longtable #165

pmtables 0.2.0

  • Add by argument to pt_cont_long so that, when panel is also passed, the table is paneled by col and is “by” the panel variable #92
  • Refactor pt_cat_long so that summary numbers are shown underneath column labels #102
  • Refactor longtable row and column spacing so that they use row and col in tab_size() with the same behavior as tabular / stable() #105
  • Add cols_extra feature, allowing extra column header information passed as a data frame (see tab_cols()) #102, #118
  • Added documentation for data arguments to reinforce that pmtables doesn’t filter or subset data prior to processing or summarizing #120
  • Fix bug in stable_long() where stable_file wasn’t getting saved
  • Add n summary column to pt_cat_wide() #80
  • Add functions that return table notes for continuous and discrete data summaries and data inventory tables #114
  • Make pt_wrap() generic; add method for stable_long that doesn’t wrap with table #121

pmtables 0.1.0

  • Adding NEWS file
  • Add duplicates_ok argument to rowpanel
  • Error if duplicate panel names found and duplicates_ok is FALSE
  • Refactor how panel groupings are determined - non-repeating values rather than unique
  • Added debug_data argument to stable; this adds an environment to the output with some data that underlies the table; the environment can be accessed with get_debug_data()
  • Added complete series of st_* functions that can be used in a pipeline to set arguments for stable(); see inst/demo-pipe.pdf
  • st2doc will render multiple page document when a list of tables is passed in as text
  • Changed stable argument from bold_cols to col_bold
  • Column names are only rendered with bold font when requested using col_bold argument
  • The prefixes for r_file and output_file are only settable with options r.file.label and output.file.label, respectively
  • Dropped col_space, row_space and fontsize arguments to stable(); they should be set with a call to tab_size
  • Add st_sizes() to set sizes argument to stable()
  • Refactor stable() function in order to reduce cyclomatic complexity and shorten overall function length in response to brief review and comment by TS representative
  • Make stable a generic function; methods for data.frame and pmtable
  • All pmtables functions now accept panel argument as a rowgroup object
  • Add as.panel() function for constructing rowgroup objects
  • For pmtables functions: when panel is passed with an alternate name, the name is is used to set the prefix
  • Fixed bug where column names were getting sanitized before rename happened #62
  • Pick up option pmtables.dir to set output directory for stable_save()
  • Pick up option mrg.script to set script name in st_files() and tab_notes()
  • Refactored the way that table cols and units are assembled; column labels are split on ... to create multi-line column names
  • Add header_row argument to tab_cols() to control the spacing between column labels and between labels and units
  • Fix warning message when trying to align a column not in the data set
  • Fix warning message when trying to add unit to column not in the data set
  • Add several new package options; see ?pt_opts
  • Add center argument to col_fixed; when ragged is no, the column can still be fixed and centered
  • Dots (...) added to st_new() / st_data() to be collected by args
  • Add st_units() pipeline function
  • Add tex_bold() function to style data frame contents
  • Add tex_it() function to style data frame contents
  • Add st_edit()
  • Refactor st_hline(); allow to add hline by regexp across whole data frame or targeted
  • Refactored st_bold and st_it to target columns or whole data frame
  • Add st_drop()
  • Add data sets analysis1, pmt_pk, pmt_first, pmt_obs
  • Change argument names for tab_cols: all col_xyz arguments are renamed to cols_xyz
  • Add find_bq_col function to allow either BQL or BLQ as default value for bq_col argument to pt_data_inventory
  • Add pattern and cols arguments to st_sumrow; this allows calculation of rows based on a regular expression
  • Add df_grep_rows and df_grepl_rows functions for finding rows where a regular expression is matched
  • Add pmtables.escape option to pass a character vector of items to be escaped
  • Unit of escape is now individual positions in a vector rather than the whole vector itself
  • No longer requiring or assuming that header_row (tab_size()) is a negative number; enter a negative number if you want to remove space between header rows; this should only be required when row space is increased